private GCBin.GCResult getBin(String chr, int gcContent) {
for (Location loc : GCBins.keySet()) {
if (loc.getChromosome().equals(chr) && loc.containsLocation(gcContent))
return GCBins.get(loc);
}
return null;
}
@Override
public DNASequence mutateSequence(String sequence, int count) {
lastMutations = new LinkedHashMap<Location, DNASequence>();
for (int i = 0; i < count; i++) {
int size = this.getRandomVarLength();
if (size >= sequence.length()) continue;
int siteStart = getStartSite(sequence.length(), size);
Location newLoc = new Location(siteStart, siteStart + size);
// need to exclude previous sites
for (Location loc : lastMutations.keySet()) {
while (loc.overlapsLocation(newLoc)) {
siteStart = getStartSite(sequence.length(), size);
newLoc = new Location(siteStart, siteStart + size);
}
}
String copySeq = sequence.substring(siteStart - size, siteStart);
StringBuffer buf = new StringBuffer();
buf.append(sequence.substring(0, siteStart));
buf.append(copySeq);
buf.append(sequence.substring(siteStart, sequence.length()));
sequence = buf.toString();
lastMutations.put(new Location(siteStart, siteStart + size), new DNASequence(sequence));
}
return new DNASequence(sequence);
}